FALL RIVER — It took nearly three hours and, at the end, Mayor Will Flanagan was the only one who didn’t vote for a $99 million school operating budget for fiscal 2015.

All other six members of the School Committee voted to adopt the $99 million figure, thereby rejecting the $97 million draft budget proposed this month by Flanagan and the city’s financial team. Flanagan said the $97 million would have level-funded services in the school district.

There were a lot of individual statements during the Friday night meeting at Morton Middle School but not much debate. School Committee members Paul Hart and Robert Maynard did not speak during the meeting.

The board’s direction was apparent early on. Almost immediately after the start of the meeting, Vice Chairman Mark Costa moved the $99 million budget figure. Committee member Melissa Panchley seconded the motion.

The budget that passed Friday night will be forwarded to the City Council for final approval.

Early in the meeting, just after Costa’s motion was made but before the vote, one of the meeting’s rare heated moments came when, shortly after she took to the podium to answer questions, Flanagan asked City Administrator Cathy Ann Viveiros if she would recommend the School Committee hold off on the vote until the city’s financial team could assemble more information.

“Why are you asking for her opinion?” Costa snapped at Flanagan. “I don’t need her recommendation.”

A motion to postpone the vote was never made, though Viveiros did recommend the postponement, saying more time would be beneficial to the fact-gathering process.

Friday’s vote came after more than two months of disagreement between city and school officials and back-and-forth discussions on questions over the schools’ projected shortfalls in state-required net school spending for fiscal 2014.

School officials project that by June 30, the School Department will have underspent its net school spending amount by $2.8 million and would need to make up that shortfall in fiscal 2015.

That shortfall came from two sources: funds that were transferred from the district’s fiscal 2014 operating budget of $91 million to cover unexpected increases in student transportation, and actual health care expenditures that have, so far, come in well below original projections.

Viveiros said the actual cost of health insurance, considered an indirect school expense, is still an unknown for 2015. She explained that the city has made payments for claims in its self-insured plan in arrears. As the city switches over to a new premium-based plan, it will still need to make two additional payments on the former plan. There will be two remaining payments to be made after June 30.

Those payments are expected to total over $3 million, which Viveiros said should cover the $2.8 million net school spending carryover.